Bake Texture from procedural Shader to multiple Objects from Array
I'm afraid the Array modifier needs to be applied before any texture baking.
Or it will only bake the original tile - which is not what you want.

Another solution:
Use Object or UV coordinates for both your textures 


the Noise Texture uses Generated coordinates, when it's not
connected to anything
but Generated coordinates change when you apply the Array modifier
use Object coordinates instead, for both textures, and they will stay the same